chr11-37568682-G-A

Variant names:

• chr11-37568682-G-A
• rs1461898

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.285 in 151,746 control chromosomes in the GnomAD database, including 6,927 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.29 (6927 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.286
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.445 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.285 AC: 43226 AN: 151624 Hom.: 6911 Cov.: 32

Gnomad AFR AF: 0.451

Gnomad AMI AF: 0.208

Gnomad AMR AF: 0.202

Gnomad ASJ AF: 0.189

Gnomad EAS AF: 0.232

Gnomad SAS AF: 0.269

Gnomad FIN AF: 0.189

Gnomad MID AF: 0.379

Gnomad NFE AF: 0.229

Gnomad OTH AF: 0.269

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.285 AC: 43281 AN: 151746 Hom.: 6927 Cov.: 32 AF XY: 0.283 AC XY: 20944 AN XY: 74126

African (AFR) AF: 0.451 AC: 18645 AN: 41360

American (AMR) AF: 0.202 AC: 3075 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.189 AC: 656 AN: 3466

East Asian (EAS) AF: 0.231 AC: 1183 AN: 5120

South Asian (SAS) AF: 0.270 AC: 1298 AN: 4810

European-Finnish (FIN) AF: 0.189 AC: 1996 AN: 10572

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.229 AC: 15555 AN: 67874

Other (OTH) AF: 0.271 AC: 572 AN: 2110

Alfa AF: 0.248 Hom.: 16328

Bravo AF: 0.291

Asia WGS AF: 0.277 AC: 961 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.39
DANN	Benign	0.56
PhyloP100		-0.29

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1461898; hg19: chr11-37590232;